From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet

Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J (2009)
NUCLEIC ACIDS RESEARCH 37(14).

Journal Article | Published | English

No fulltext has been uploaded

Author
; ; ; ;
Abstract
Year by year, approximately two million people die from tuberculosis, a disease caused by the bacterium Mycobacterium tuberculosis. There is a tremendous need for new anti-tuberculosis therapies (antituberculotica) and drugs to cope with the spread of tuberculosis. Despite many efforts to obtain a better understanding of M. tuberculosis' pathogenicity and its survival strategy in humans, many questions are still unresolved. Among other cellular processes in bacteria, pathogenicity is controlled by transcriptional regulation. Thus, various studies on M. tuberculosis concentrate on the analysis of transcriptional regulation in order to gain new insights on pathogenicity and other essential processes ensuring mycobacterial survival. We designed a bioinformatics pipeline for the reliable transfer of gene regulations between taxonomically closely related organisms that incorporates (i) a prediction of orthologous genes and (ii) the prediction of transcription factor binding sites. In total, 460 regulatory interactions were identified for M. tuberculosis using our comparative approach. Based on that, we designed a publicly available platform that aims to data integration, analysis, visualization and finally the reconstruction of mycobacterial transcriptional gene regulatory networks: MycoRegNet. It is a comprehensive database system and analysis platform that offers several methods for data exploration and the generation of novel hypotheses. MycoRegNet is publicly available at http://mycoregnet.cebitec.uni-bielefeld.de.
Publishing Year
ISSN
eISSN
PUB-ID

Cite this

Krawczyk J, Kohl TA, Goesmann A, Kalinowski J, Baumbach J. From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH. 2009;37(14).
Krawczyk, J., Kohl, T. A., Goesmann, A., Kalinowski, J., & Baumbach, J. (2009). From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH, 37(14).
Krawczyk, J., Kohl, T. A., Goesmann, A., Kalinowski, J., and Baumbach, J. (2009). From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH 37.
Krawczyk, J., et al., 2009. From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH, 37(14).
J. Krawczyk, et al., “From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet”, NUCLEIC ACIDS RESEARCH, vol. 37, 2009.
Krawczyk, J., Kohl, T.A., Goesmann, A., Kalinowski, J., Baumbach, J.: From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet. NUCLEIC ACIDS RESEARCH. 37, (2009).
Krawczyk, Justina, Kohl, Thomas A., Goesmann, Alexander, Kalinowski, Jörn, and Baumbach, Jan. “From Corynebacterium glutamicum to Mycobacterium tuberculosis-towards transfers of gene regulatory networks and integrated data analyses with MycoRegNet”. NUCLEIC ACIDS RESEARCH 37.14 (2009).
This data publication is cited in the following publications:
This publication cites the following data publications:

19 Citations in Europe PMC

Data provided by Europe PubMed Central.

CMRegNet-An interspecies reference database for corynebacterial and mycobacterial regulatory networks.
Abreu VA, Almeida S, Tiwari S, Hassan SS, Mariano D, Silva A, Baumbach J, Azevedo V, Rottger R., BMC Genomics 16(), 2015
PMID: 26062809
Role of intragenic binding of cAMP responsive protein (CRP) in regulation of the succinate dehydrogenase genes Rv0249c-Rv0247c in TB complex mycobacteria.
Knapp GS, Lyubetskaya A, Peterson MW, Gomes AL, Ma Z, Galagan JE, McDonough KA., Nucleic Acids Res. 43(11), 2015
PMID: 25940627
Genomic mapping of cAMP receptor protein (CRP Mt) in Mycobacterium tuberculosis: relation to transcriptional start sites and the role of CRPMt as a transcription factor.
Kahramanoglou C, Cortes T, Matange N, Hunt DM, Visweswariah SS, Young DB, Buxton RS., Nucleic Acids Res. 42(13), 2014
PMID: 24957601
Genome-scale bacterial transcriptional regulatory networks: reconstruction and integrated analysis with metabolic models.
Faria JP, Overbeek R, Xia F, Rocha M, Rocha I, Henry CS., Brief. Bioinformatics 15(4), 2014
PMID: 23422247
In silico analyses for the discovery of tuberculosis drug targets.
Chung BK, Dick T, Lee DY., J. Antimicrob. Chemother. 68(12), 2013
PMID: 23838951
CoryneRegNet 6.0--Updated database content, new analysis methods and novel features focusing on community demands.
Pauling J, Rottger R, Tauch A, Azevedo V, Baumbach J., Nucleic Acids Res. 40(Database issue), 2012
PMID: 22080556
The regulation of sulfur metabolism in Mycobacterium tuberculosis.
Hatzios SK, Bertozzi CR., PLoS Pathog. 7(7), 2011
PMID: 21811406
Computational tools to study and understand the intricate biology of mycobacteria.
Sharma D, Surolia A., Tuberculosis (Edinb) 91(3), 2011
PMID: 21398182
Diversity of metabolic shift in response to oxygen deprivation in Corynebacterium glutamicum and its close relatives.
Yamamoto S, Sakai M, Inui M, Yukawa H., Appl. Microbiol. Biotechnol. 90(3), 2011
PMID: 21327408
Mutations in the regulatory network underlie the recent clonal expansion of a dominant subclone of the Mycobacterium tuberculosis Beijing genotype.
Schurch AC, Kremer K, Warren RM, Hung NV, Zhao Y, Wan K, Boeree MJ, Siezen RJ, Smith NH, van Soolingen D., Infect. Genet. Evol. 11(3), 2011
PMID: 21277396
Cyclic AMP signalling in mycobacteria: redirecting the conversation with a common currency.
Bai G, Knapp GS, McDonough KA., Cell. Microbiol. 13(3), 2011
PMID: 21199259
Comparative genomics of NAD(P) biosynthesis and novel antibiotic drug targets.
Bi J, Wang H, Xie J., J. Cell. Physiol. 226(2), 2011
PMID: 20857400
Systems biology approaches to understanding mycobacterial survival mechanisms.
Boshoff HI, Lun DS., Drug Discov Today Dis Mech 7(1), 2010
PMID: 21072257
Structural and functional analysis of Rv0554 from Mycobacterium tuberculosis: testing a putative role in menaquinone biosynthesis.
Johnston JM, Jiang M, Guo Z, Baker EN., Acta Crystallogr. D Biol. Crystallogr. 66(Pt 8), 2010
PMID: 20693690
Tuberculosis: global approaches to a global disease.
Kirschner DE, Young D, Flynn JL., Curr. Opin. Biotechnol. 21(4), 2010
PMID: 20637596
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes.
Novichkov PS, Laikova ON, Novichkova ES, Gelfand MS, Arkin AP, Dubchak I, Rodionov DA., Nucleic Acids Res. 38(Database issue), 2010
PMID: 19884135
Role of the transcriptional regulator RamB (Rv0465c) in the control of the glyoxylate cycle in Mycobacterium tuberculosis.
Micklinghoff JC, Breitinger KJ, Schmidt M, Geffers R, Eikmanns BJ, Bange FC., J. Bacteriol. 191(23), 2009
PMID: 19767422

69 References

Data provided by Europe PubMed Central.

Structural and biochemical analysis of the Rv0805 cyclic nucleotide phosphodiesterase from Mycobacterium tuberculosis.
Shenoy AR, Capuder M, Draskovic P, Lamba D, Visweswariah SS, Podobnik M., J. Mol. Biol. 365(1), 2007
PMID: 17059828
New messages from old messengers: cAMP and mycobacteria.
Shenoy AR, Visweswariah SS., Trends Microbiol. 14(12), 2006
PMID: 17055275
Mycobacterial adenylyl cyclases: biochemical diversity and structural plasticity.
Shenoy AR, Visweswariah SS., FEBS Lett. 580(14), 2006
PMID: 16730005
Expression of Corynebacterium glutamicum glycolytic genes varies with carbon source and growth phase.
Han SO, Inui M, Yukawa H., Microbiology (Reading, Engl.) 153(Pt 7), 2007
PMID: 17600063
Characterization and use of catabolite-repressed promoters from gluconate genes in Corynebacterium glutamicum.
Letek M, Valbuena N, Ramos A, Ordonez E, Gil JA, Mateos LM., J. Bacteriol. 188(2), 2006
PMID: 16385030
Genome scale portrait of cAMP-receptor protein (CRP) regulons in mycobacteria points to their role in pathogenesis.
Akhter Y, Yellaboina S, Farhana A, Ranjan A, Ahmed N, Hasnain SE., Gene 407(1-2), 2008
PMID: 18022770
WebLogo: a sequence logo generator.
Crooks GE, Hon G, Chandonia JM, Brenner SE., Genome Res. 14(6), 2004
PMID: 15173120
Macro-array and bioinformatic analyses reveal mycobacterial 'core' genes, variation in the ESAT-6 gene family and new phylogenetic markers for the Mycobacterium tuberculosis complex.
Marmiesse M, Brodin P, Buchrieser C, Gutierrez C, Simoes N, Vincent V, Glaser P, Cole ST, Brosch R., Microbiology (Reading, Engl.) 150(Pt 2), 2004
PMID: 14766927
Genes required for mycobacterial growth defined by high density mutagenesis.
Sassetti CM, Boyd DH, Rubin EJ., Mol. Microbiol. 48(1), 2003
PMID: 12657046
A postgenomic method for predicting essential genes at subsaturation levels of mutagenesis: application to Mycobacterium tuberculosis.
Lamichhane G, Zignol M, Blades NJ, Geiman DE, Dougherty A, Grosset J, Broman KW, Bishai WR., Proc. Natl. Acad. Sci. U.S.A. 100(12), 2003
PMID: 12775759
Genome-wide requirements for Mycobacterium tuberculosis adaptation and survival in macrophages.
Rengarajan J, Bloom BR, Rubin EJ., Proc. Natl. Acad. Sci. U.S.A. 102(23), 2005
PMID: 15928073
Characterization of a Mycobacterium tuberculosis H37Rv transposon library reveals insertions in 351 ORFs and mutants with altered virulence.
McAdam RA, Quan S, Smith DA, Bardarov S, Betts JC, Cook FC, Hooker EU, Lewis AP, Woollard P, Everett MJ, Lukey PT, Bancroft GJ, Jacobs Jr WR Jr, Duncan K., Microbiology (Reading, Engl.) 148(Pt 10), 2002
PMID: 12368431
Persistence of Mycobacterium tuberculosis in macrophages and mice requires the glyoxylate shunt enzyme isocitrate lyase.
McKinney JD, Honer zu Bentrup K, Munoz-Elias EJ, Miczak A, Chen B, Chan WT, Swenson D, Sacchettini JC, Jacobs WR Jr, Russell DG., Nature 406(6797), 2000
PMID: 10963599

Export

0 Marked Publications

Open Data PUB

Web of Science

View record in Web of Science®

Sources

PMID: 19494184
PubMed | Europe PMC

Search this title in

Google Scholar